Which windows version are you talking about?
I don't think that your approach will work (for programs). Wine simulates windows. So you still have to install the programs under wine (as far as I understand it).
It's the same as having Win98SE alongside WinXP. If MS office is installed under Win98SE, it will not run by invoking it from within WinXP (and vice versa); you still have to install it under the other OS.
I've used Xandros once (evaluation version). It came with CrossOver office (something like wine, but tailored to Office apps). I had to install MS Office inside CrossOver office, and I assume that this will be the same if you want to use wine.
In that case it will be useless to create a full FAT32 partition (unless you use Win95/Win98(SE)/WinME as you can only use FAT32). I suggest that you create a NTFS partition for Windows and apps and a FAT32 partition for sharing.
In windows, you can move your 'my documents' to this partition (right click on the 'my documents' icon and choose properties).
Please note that FAT32 does not have user permissions etc, so any windows user can access it. Within Linux, you can still limit access to the partition
if you want to do so.
wine user guide